Subject B
by TARDISful
Summary: The Doctor just lost Amy and Rory, so when a young girl he meets says she can see his past companions he is naturally interested, but who is she?
1. Chapter 1

The girl was walking with a backpack on. She glanced over her shoulder, looking out for a pursuer. The sound of the trees stirring made her jump. It wasn't just that, there was one of the weirdest noises; it made her shiver and hide behind a bush. The noise stopped and she peered around to see a blue police box had appeared. A man leaped out. He was skinny and was wearing a fez. A FEZ! He wore a brown suit jacket, black pants and a red bowtie that stood out like his suspenders on his white shirt. She edged forward as he pulled something out of his pocket and started sweeping it through the air. It buzzed and he paused as it swept past her bush and then he slipped it back into his pocket.

He walked over and started saying, "I know you're there, I picked you up on my sonic screwdriver. That's that metal thing. Hello, I am not going to harm you."

She shifted as she heard him stop behind the bush and decided that there was no point in just sitting there. "That's what they all say: I won't hurt you, well you won't trick me I will not be taken again, not again." The girl said.

The man sighed and shifted, "If I wanted to take you I would have, you're not running and you are sitting behind a bush. So are you going to come out or am I going to have to come round?"

She rose, "I'm coming."

He was standing there smiling and as she looked, she saw another man in his place. This man was wearing a blue suit, a long brown coat and had spikey hair. He changed again, then again, then again, he changed eleven times in total. She staggered backwards then blinked until he came back into focus but he was not alone. Now behind him were faint images, some clearer than others, she estimated about thirty-seven. The two clearest were a girl with red hair and a boy with brown hair. She then saw the box flicker with different designs before she fainted.

"Well that went well," Muttered the Doctor.

Thea opened her eyes and groan in pain because of the hard ground beneath her. She glanced to her write qukly and saw the man there next to a console.

"Hey, it's good to see you conscious. I have no idea why you fainted so I took you into the TARDIS, that's the big blue box."Said the man.

She sat up from where she was lying on the floor. Looking around at the massive room she saw it changing too, circles appeared on the walls, the room kept on seeming to change shape.

"STOP IT, JUST STOP IT" she screamed out and ran to the ever changing door. She ripped it open to find they were floating above the earth; she threw herself backwards in an attempt to stop falling out. She felt a hand grab the back of her shirt and pull her back in, just as her feet slipped.

"Well, I was hoping you would be impressed or surprised, or you could have said that line…. Though I think you're one of the first to almost fall out of the TARDIS, well done. Also may I ask what needs to be stopped?" The man said sitting her back on the floor, He glanced at her and saw she had her eyes closed. "Are you ok?"

She shook her head, "I need to get out of this box it has too many pasts, to many different versions. Get me out of here; put me back on that planet." She pointed in the general direction of the door.

"Oh, I thought you were trying to run away, I guess I could. Where would you like me to drop you, and more importantly, when?" She heard him running to the control panel and start flicking switches.

"When? What do you mean when…. Wait this is a time machine, cool. I must ask you to put on a general, elemental setting. Most things have one. I need it to have no past forms, unlike the current one that has many." She rose finding the rail and dragged herself up the stairs. She heard the man sigh

"But the underlying setting is no fun, all boring and simple." He flicked a few switches as the girl found her way into his chair.

"There you go the most boring setting it has, never used this before and activate." He hit a button with a loud bang and the girl fell down, the chair was gone.

"Thanks for warning me" she said as she stood up opening her eyes and brushing herself off. "Thanks. I get a horrible headache when things change a lot. Or faint, that was a first." He gave her a weird look,

"Well, glad that's sorted now where am I dropping you?" He said looking around unimpressed by his surroundings. He looked at her again and saw her staring at him with a glazy look. "What?" he asked. She blinked looked around him in the same out-of-it look.

"Who are these people and why are you changing like that. You are one person with many faces and I can't do it… please get me out of here." She broke the gaze and took a few steps back. The man glanced around,

"What people, and how are you seeing my other regenerations. Are they my companions, my friends?" He spun and starred around him. He turned back to her as she sank to the ground.

"It's a gift." she muttered starring at the ground. "Do you think you put up mental walls blocking off the past you's and your companions. I can't look up at you until you do so." She looked at the floor around her.

"Sure give me a minute." He sank down too and sat silently for a minute before he stood up. "Done." He said after he had move around a bit. She looked up and saw the man she first saw with a smile she said; "Thanks."

He smiled back "That's okay, let's start over. I'm the Doctor."

She rose and said; "Timothea Lady Doctor."


	2. Chapter 2

**Hello Readers, Thanks to the reviews, I hope I fixed what needed fixing.**

**Thanks to those who followed and those who Favorited, it means a lot (Seeing as though this is my first ever fanfic).**

**Enjoy :)**

**TARDISful**

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Chapter Two

"Ma'am, Subject B has disappeared; she went into a freak time/space anomaly. The same disturbance was then found floating in space above Australia, we picked up four heartbeats, two are its. It is currently flying down towards Cardiff. We are sending a SWAT Team to pick it up." The man fixed his glasses and handed a severe looking woman a couple of sheets of paper which she glanced down at uncaringly.

"Make sure you get it back, we can't afford to lose it like we did with its Maternal Carer." The woman said. She started walking down the rows of computers making sure everyone was working hard.

"Of course, Ma'am, we are ready to dissect it when it returns."

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"Sorry, did you just say that your last name was Doctor… weird. And I must say Lady is a weird middle name. Sorry, rambling. I may do it a bit because I have none of my past me's or companions to influence me. I must say though, seeing people who were me and have been with me is a very Time Lord thing…" The Doctor faded out and gave her the strangest look, like he was hoping but too scared to believe. "Never mind, now where am I dropping you Timothea?" He stopped at her name and gave her another look.

"I prefer to be called Thea, only my mum called me Timthie. She was great. She isn't with me any more…." The girl sighed and started walking around the controls.

"Did she die?" the Doctor asked.

"No, she just changed. She ran from the experiments like I am doing now. I miss her." Thea walked over and leaned against the blank wall.

"Sorry. Changed…. Have you seen anyone else with the many bodies like me?" he inquired, as the strange noise she first heard started again.

"Yeah, my mother, after she changed there was another one. What is that noise, it's beautiful." She closed her eyes and let the noise envelope her, but the doctor wasn't having that.

"Your mother… There was another one, like I had many; she was similar to me with the many." He franticly talked and walked closer. She opened her eyes and saw a woman standing behind him,

"Your walls are breaking dow…." She stopped as she realised who the woman was. "My mum, she was with you in her first form."

Thea stumbled forward and stared at where she saw her mother. Suddenly, the image of her mother slumped to the ground and was in the arms of the second Doctor she had seen. She felt a tear fall… "Mum, she was shot. She died in your arms, who are you? Why were you with her?" She sank next to the image she saw of her mother, who was now lying on a simple white bench. She turned as a hand rested on her shoulder.

"Jen… Jenny is your mother. Jenny, Jenny my daughter, is your mother," he stuttered, as recognition floated on to his face. "Wait." He walked back and forth in an attempt to focus on what was going on. "You are Jenny's daughter, yes?" He paused for her response.

"Yes, Jenny Lady Doctor is her full name." she said, wiping her eyes.

"Okay, you say she has been through two regenerations, three bodies?" He started walking again.

"Yes, she has. I was born to her second." She sat up as the wall went back up and the image behind her disappeared. She looked at the pacing man and saw him flickering between the man in the suit that was with her mother and his current self. Finally he stopped, turned to her and paused to fix his walls.

"Thea… Timothea, the female name for Timothy or Tim. Tim…Time. You are my granddaughter, Thea my granddaughter. I… how, Jenny died!" His smile died, he lost his excitement. "I've gone mad. I saw Jenny die. Who are you, how can you be here?" He started to raise his voice and walked up to her with fury in his eyes.

"She told me her story. She said she revived, that she went exploring the universe. She found her way to Earth where she was taken in for experiments. The first set of them killed her, she changed. Then she had me. She was put back in to experimentation and that killed her again, she changed again. This time she wasn't very caring. She ran away, leaving me behind. I still love her, she just left." As Timothea spoke she took a step towards The Doctor, her confidence growing. "My Mother, your daughter, lives. She is out there living her life in fear and you know who I blame… you! If you had been a better father, stayed with her for longer you would have been able to keep her safe. You could have made sure she was not in trouble. You could have been a DAD!" Her voice raised and The Doctor took a few steps back.

"Sorry, I saw her die. I left her with some of my friends for a proper burial. I never knew." The Doctor said quietly, scared even.

"Grandfather, I have a grandfather. Now drop me off Pa, can I call you Pa? We have a woman to find." Thea's anger disappeared; she let out a smile, gave The Doctor a hug and ran to stand by the door.

"Right, Cardiff is right outside those doors, let's go Timthie."The Doctor smiled and clicked his fingers opening the doors wide. "Let's go find Jenny."

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"Soldiers prepare!" The SWAT team gathered around the box that had just landed in the middle of Cardiff. The doors swung open and Subject B and a man stepped out, arms linked and smiles on their faces. "SWAT team move in," came a shout and men came out of nowhere, grabbing the girl and the man, surrounding the box. The man managed to click his fingers and the doors of the box slammed closed. A truck rolled in and the two people were thrown inside. The box was lifted in by a machine and the doors of the truck snapped shut. The Doctor, the TARDIS and Thea were caught.


	3. Chapter 3

**Hello Everyone,**

**I am hoping your enjoying my story.**

**I was going to post on Sunday because 'Deep Breath' came out (Australia) but I couldn't find my USB. So here is it now.**

**I am excited for the new doctor (Capaldi will be brilliant) and am hoping that all you are satisfied.**

**I am going to start this line with 'I' because I started all the other ones with 'I'. What do you think about the new episode/doctor?**

**Hope you enjoy!**

**TARDISful**

**P.S. I am considering letting Thea (Jenny) see Capaldi but I not sure. As some of you have worked out Thea saw the War Doctor and i think both of them should see the future selves. But would it work.**

**P.P.S. I am going to redo chapter one with proper paragraphing and editing and tenses and stuff**

Chapter Three

The Doctor rose back into consciousness, he looked around to find he was in a cell. He let the world come into focus and realised that the furious sound of sobbing had brought him back. Thea was in the cell next to him sobbing uncontrollably. "Thea, are you ok. I'm here right here next door. Timthie..." He rose and went to the bars between their cells. "…listen to me I'll get us out. You and I will get away. We'll run to the TARDIS and we will go and find your mother." The doctor spoke desperately "Thea please." He begged when she did not respond.

"Doctor there is no hope. I am to be put under the same experiments that killed my mum. I'm dead." She wiped her eyes. "I can't get out and if my mother left why would she want to see me again. She left to save herself, she didn't take me." Thea let anger slip into her voice.

"Thea, what if she left to get help, What if she is on her way back to save you. Thea..." he pulled out his sonic screwdriver, and checked to see if anyone was around. "... Your hero is here." He rose the sonic and pointed it at the lock. The lock exploded open and The Doctor promptly did the same to her lock. "Let's go" The Doctor ran round to help her out. They ran down the corridor past cell after cell, all empty. Suddenly two large, muscular men stepped out and grabbed them both.

"Nice try, what is that thing a sonic probe." A voice echoed over an intercom. "Like we would let you get away. Bring them to the lab." The intercom cut out and the men started dragging them away.

"Sonic Screwdriver!" The Doctor shouted out. Thea and the Doctor were taken through a series of corridors and then led into a large lab with two tables in the middle. On one side there was a small, cell like room. The whole place was a pristine glaring white.

"Hand over the sonic probe." One of the men held out his hand for it. The doctor handed it over,

"Sonic Screwdriver." He muttered.

"It does not matter what it is, it is no longer authorised." The man threw the screwdriver into a chute labelled 'incinerator', the other one was currently tying Thea to one of the tables. The Doctor was thrown in to the cell room and a woman walked, she was tall and had short brown hair. She came in with an air of authority.

"Subject B nice to see you again," she began and was cut short as Thea spat at her. "Happy to see you too," she continued "and who do we have here, we picked up four heart beats one is yours unless…" she pulled a scanner out of her pocket and held it up in front of her pointing towards the Doctor. It began to beep frantically. "Two heart beats, well, well, well, I'm glad we caught you as well, a male specimen. We have some experiments to run on you." Some people in white suits came into the room dragging a tray of gruesome instruments. Thea screamed in horror.

Jenny recalled how she had run from this place a year ago. The Alienceop Institute. Now she was back, breaking in to save her daughter. She was now in the same room as her, disguised as a scientist. Jenny scanned the room, she saw a man locked in the side cell, and he was wearing some ridiculous clothes. Then her eyes fell upon Thea, strapped to the table like she had once been. She needed a plan and she needed one now. Thea's scream sent shivers down her spine. _I'll help you Timthie_, was all that was in her head. The other people around her started getting their various tools ready. She stumbled forward and grabbed the sharpest tool she could find. The scientist started taking their places around Thea, Jenny quickly hurried to get near one of the straps restraining her daughter. As Professor Lilith, who was in charge, started telling them all, the man as well what was happening. Jenny let her hands casually drop as she listened. Everyone was focused on Lilith, so Jenny decided it was safe to start cutting the straps. Thea focussed on her and Jenny casually, as possible, put two fingers up and made them move like a beating heart, two hearts. Thea's eyes widened with question, Jenny nodded once. _Hold Still_ Jenny willed Thea to hear. Jenny snapped back to attention when Lilith mentioned Subject A, Her. _I'm okay she was just talking about the information they got from me._ The strap was tight to the table and it took some effort to get the scalpel underneath it. The strap cut easily and Jenny quickly grabbed it and pulled it tight to ensure it still looked fixed. Thea reached for it and held so that Jenny could cut the rest_. On to _the _last One, _the scientist next to her gave her a weird look as she took a step sideways to reach the final strap. She pretended that she had lost her balance and 'regained it'. This strap was the hardest it was tight to her shoulders and it was almost impossible to get the scalpel underneath. The blade cut in to Thea's clothes and Jenny saw a drop of blood appear.

"Now scientist, of mine," Lilith voice came in to focus. "The dissection can begin. Find out everything we need." Jenny yanked the blade towards her, snapping the strap. .

Jenny grabbed Thea's hand; "Run!"

Thea leapt to her feet and started running towards the door with her mother. The scientist grabbed for them, none caught them. As they reached the door Thea turned around to see the Doctor leaning into the bars containing him. They were leaving without him. Lilith pointed a gun in the Doctor's direction, smiling evilly. Jenny yanked Thea towards the door.

She screamed as the gun went off "Doctor!"

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**I am hoping you enjoyed and also that I left you with suspense.**

**Please Review**


	4. Chapter 4

**Hello Readers, **

**Here is a chapter (Finally)**

**Okay just warning you there is mention of blood and bullet wounds in this chapter. (Spoilers!) **

**I am on holidays so i will try and write as much as i can but hey its hard.**

**Thanks For Reading, Reviewing, Favouriting and Following**

**TARDISful :)**

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Jenny kept running, dragging Thea along.

"Mum please. The Doctor needs us. He needs us mum." Thea screamed at her mother trying to drag her back to the lab. It was no use; Jenny was overly strong because she was born for war. As they ran towards the exit they passed occupied cells. Inside were people, Timelords. They had been bred from Thea's and Jenny's genes, Genetic anomalies. The Timelords moaned and cried for help.

"Timothea, Jenny save us."

"You're our parents, help us."

"Why are you leaving us?!"

Jenny ran faster, ignoring the cries. Tears ran down Thea's cheeks as she glanced in to the cells and saw children. They reached the door at the other side of the corridor and just as they were stepping out some one cried;

"You are our parents and you leave us to die, and with that knowledge we curse you. You leave another as well someone you are closer to, The Doct..."

Jenny slammed the door before he could finish. They ran on, seeing the exit. Jenny sped up, trying to reach it before they were caught. They were not far from the door when someone ran through the doors at the end of the corridor.

"Halt or we will shoot." A man's voice called to them.

They reached the door and turned to face two men both holding guns up at them. Jenny reached behind her and started fiddling with the door, trying to get it open.

"Come with us, now." The man took a step to the side, giving a clear passage to the door back to the lab.

Jenny pulled a pin out of her long brown hair and started to pick the lock.

"You can't shoot us, you need us peek physical condition and healthy. So no, we're not coming." Jenny talked almost laughing as the men expressions change to annoyance. They took a step closer to the girls.

"Don't even." Thea said stepping forwards and sinking in to a classic martial art position.

The men paused, then put down their guns and stood to face Thea. "Do you really want to go?"

"Fighting; no, Leaving; hell yeah," Thea raised her arms and prepared to fight.

"Be careful, Thea." Jenny whispered still working on the lock. "Boys don't you think it's a bit stupid to have locks on both sides?" She paused to address the guards.

"It stops break ins and break outs." One of them answered.

"Well no it doesn't" Jenny said and a quiet click sounded as the lock opened.

Thea leaped forward tripping the men and grabbing their guns. "Sorry boys we're out of here." Thea said as she and Jenny walked out. "Gun mother?" Thea said offering it to Jenny.

"Thanks, Thea." Jenny said in a hard tone taking the gun and speeding up in to a jog.

They ran on for a while until the Institute was out of sight, they found themselves in an abandoned work yard.

"The Doctor, you said the Doctor." Jenny said turning to Thea with a look of worry. "Is it _The Doctor _or a Doctor? My father Doctor or random doctor."

Thea swallowed tears starting to show in her eyes. "The Doctor mum, He saved me from the institute and then we both got captured. They want to experiment on him like they did to us. He... I think he got shot as we were leaving. We have to go back and save him. "

Thea was properly crying now, tears dripping off her chin. Jenny put down her gun and did something she hadn't done in years, she hugged Thea. Not a quick awkward hug but a proper hug meant to comfort and relax. "Okay Thea, we'll save him. We'll find a way." Jenny spoke ending the hug and kissing Thea on the head. "We just need a plan."

Jenny went and picked up her gun.

"Thanks mum" Thea said smiling weakly up at her. Noticing her changing form for the first time, it was faint and didn't bother her.

"Well now it's time you and I go meet my friend. He'll help us, oh and he knows the doctor." Jenny spoke leading Thea to a tarp covered shape. Jenny pulled the tarp and underneath was a old beaten up car. "Off we go." Jenny said Jumping into the driver's side.

Thea gave the car a look of worry before hopping in. "are you sure this is safe." She asked pulling on her fraying seat belt.

"It got me here;" Said Jenny as she pulled out a key and tried her hardest to fit it in the bashed up key hole. As it went in she had to put a lot of effort in to turning it. "Sorry for the delay, tis car has seen better days."

The engine started and Jenny slowly drove them out on to the main road.

"Let's Go." Thea Muttered gripping the edge of her seat.

The Doctor woke up in the prison cell he was in before the lab. Sitting up he glanced around looking for Jenny and Thea. He groaned feeling pain in his left heart. He looked down at his shirt and saw a blood stain and a hole.

"Got shot, well done."

He groaned again as he pulled off his bow tie and shirt to inspect the damage. There was a line of stitching on his chest; they had operated on him to keep him alive.

"Oww."

He said placing his hand over the stitching deciding he could waste a bit of his life to fix himself. His hand shone with regeneration energy as he repaired himself. Once he had finished he pulled his shirt back on, fixed his suspenders and re-did his bowtie.

"Right that's done now what." He muttered finding his jacket in the corner. He pulled it back on looking around for a way out.

"You come with us." Professor Lilith said walking in to the corridor of cells.

"Why would I do that?"Asked The Doctor Standing up and walking towards the front of the cell.

"You will because you have no choice in the matter." She spoke as two guards walked in unlocked his cell and dragged him out.

"Okay well looks like I am coming." He said trying to convince them he was calm.

"Nice trick with the healing by the way, how did you do it?" The Professor kept talking leading them back towards the lab.

"I'm a Timelord." Said The Doctor "I believe you already knew that though."

"A Timelord, we just called you species _duo cordisians, _but I think I like Timelord. Thank You Doctor." She spoke in a taunting manner. "We are glad we captured you."

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**Hope you enjoyed!**

**Sorry about the blood again.**

**I wonder who Jenny's Friend could be. (Check Description.)**

**I am re-posting chapter one and deleting the first bit, i was going to do something clever but gave up. **

**Thanks Again For everything**

**TARDISful :)**


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